Aniseed - Cis-regulation

Cis-regulatory Region

Name

Ci-MLC2 -53/61 4 M2 added

Short name

n/a

Region ID

REG00000088

Status

Curated

Origin

engineered region from C. robusta formely Ciona int. type A

Type of Activity

regulatory_region
(enhancer)

Author

Kusakabe team (2007-01-28)

Annotator

Jonathan Luchino (2007-05-15)

Curator

Delphine Dauga (2010-04-08)

View position in WashU

Description

The M2 motifs present in the enhancer sequence upstream the +1 of transcription of the Ci-MLC2 gene are necessary and sufficient for the expression in the muscle cells.

Be careful, coordinates in the paper are different from ANISEED coordinates. We took the KH transcript model as reference.

Coordinates in the paper : -115bp/-1bp

Hierarchy of Regulatory Regions

Modification of Ci-MLC2 -53/61 by insertion

Ci-MLC2 -438/205 REG00000006 [ regulatory_region (extended_promoter) ]

Regulated gene(s)

KH2012:KH.C1.20 (MYL1; MYL4; MYL6B)

Construct(s) made to test this region

CONS00000078: pMLC2 -53/61 4 M2d added::GFP

Show in situ data

Overview of functional TF binding sites in this region

7,191,2587,191,379

	Binding Factor(s)	Sequence	Position in Region
1	n/a	TTCTCACGTCACT	[-53 / -41]
2	n/a	TTCTCACGTCACT	[-40 / -28]
3	n/a	TTCTCACGTCACT	[-27 / -15]
4	n/a	TTCTCACGTCACT	[-14 / -2]

Sequence

Aniseed Coordinates: [7,191,258 / 7,191,379] on scaffold KhC1

This sequence was found with a blast on the JGI site with the sequence includes in the publication listed bellow, like the sequences of the motifs.

Show sequence

Length: 166

TTCTCACGTCACTTTCTCACGTCACTTTCTCACGTCACTTTCTCACGTCACTTATCAGGT
CATTATGTCTGTTATAAAAGCGCTGGGTCGAAGTTTAACAGCATTCAGTTCTGCTTAAGC
ATAATCTAGCAAGCATCAAACATCCTTCAAGACGATAAACTATTAT

Reference(s)

Kusakabe et al. (2004). Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona. Dev. Biol. 276(2):563-80